{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T13:26:18Z","timestamp":1760189178197},"reference-count":28,"publisher":"Springer Science and Business Media LLC","issue":"S1","license":[{"start":{"date-parts":[[2011,2,15]],"date-time":"2011-02-15T00:00:00Z","timestamp":1297728000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"DOI":"10.1186\/1471-2105-12-s1-s5","type":"journal-article","created":{"date-parts":[[2011,2,18]],"date-time":"2011-02-18T15:02:28Z","timestamp":1298041348000},"source":"Crossref","is-referenced-by-count":10,"title":["FPGA accelerator for protein secondary structure prediction based on the GOR algorithm"],"prefix":"10.1186","volume":"12","author":[{"given":"Fei","family":"Xia","sequence":"first","affiliation":[]},{"given":"Yong","family":"Dou","sequence":"additional","affiliation":[]},{"given":"Guoqing","family":"Lei","sequence":"additional","affiliation":[]},{"given":"Yusong","family":"Tan","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,2,15]]},"reference":[{"key":"4363_CR1","unstructured":"The growth of the protein sequence in UniProtKB\/TrEMBL - Current Release Statistics[\n                    http:\/\/www.ebi.ac.uk\/uniprot\/TrEMBLstats\/\n                    \n                  ]"},{"key":"4363_CR2","unstructured":"Yearly growth of total structures in the Protein Data Bank (PDB)[\n                    http:\/\/www.pdb.org\/pdb\/statistics\/contentGrowthChart.do?contecnt=totaln&seqid=100\n                    \n                  ]"},{"key":"4363_CR3","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1006\/jcph.1999.6200","volume":"151","author":"R Sanchez","year":"1999","unstructured":"Sanchez R, Sali A: Corparative protein structure modeling in genomics. J. Comput. Phys 1999, 151: 388\u2013401. 10.1006\/jcph.1999.6200","journal-title":"J. Comput. Phys"},{"key":"4363_CR4","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1038\/358086a0","volume":"358","author":"DT Jones","year":"1992","unstructured":"Jones DT, Taylor WR, Thornton JM: A new approach to protein fold recognition. Nature 1992, 358: 86\u201389. 10.1038\/358086a0","journal-title":"Nature"},{"key":"4363_CR5","doi-asserted-by":"publisher","first-page":"4436","DOI":"10.1073\/pnas.91.10.4436","volume":"91","author":"JU Bowie","year":"1994","unstructured":"Bowie JU, Eisenberg D: An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function. Proceedings of the National Academy of Sciences of the United States of America 1994, 91: 4436\u20134440. 10.1073\/pnas.91.10.4436","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"4363_CR6","first-page":"211","volume":"13","author":"P Chou","year":"1974","unstructured":"Chou P, Fasman G: Prediction of protein conformation. Biopolymers 1974, 13: 211\u2013215.","journal-title":"Biopolymers"},{"key":"4363_CR7","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/0022-2836(78)90297-8","volume":"120","author":"J Garnier","year":"1978","unstructured":"Garnier J, Osguthorpe DJ, Robson B: Analysis and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol 1978, 120: 97\u2013120. 10.1016\/0022-2836(78)90297-8","journal-title":"J. Mol. Biol"},{"key":"4363_CR8","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1016\/S0076-6879(96)66034-0","volume":"266","author":"J Garnier","year":"1996","unstructured":"Garnier J, Gibrat JF, Robson B: GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol 1996, 266: 540\u2013553. full_text","journal-title":"Methods Enzymol"},{"key":"4363_CR9","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1002\/pro.5560040401","volume":"4","author":"KA Dill","year":"1995","unstructured":"Dill KA: Principles of protein folding - a perspective from simple exact models. Protein Sci 1995, 4: 561\u2013602. 10.1002\/pro.5560040401","journal-title":"Protein Sci"},{"key":"4363_CR10","doi-asserted-by":"publisher","first-page":"502","DOI":"10.1002\/1097-0134(20000815)40:3<502::AID-PROT170>3.0.CO;2-Q","volume":"40","author":"JA Cuff","year":"2000","unstructured":"Cuff JA, Barton GJ: Application of enhanced multiple sequence alignment profiles to improve protein secondary structure. Proteins: Struct. Funct. Genet 2000, 40: 502\u2013511. \n                    Publisher Full Text\n                    \n                   10.1002\/1097-0134(20000815)40:3<502::AID-PROT170>3.0.CO;2-Q","journal-title":"Proteins: Struct. Funct. Genet"},{"key":"4363_CR11","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1016\/S0022-2836(05)80333-X","volume":"216","author":"RD King","year":"1990","unstructured":"King RD, Sternberg MJE: A machine learning approach for the prediction of protein secondary structure. J. Mol. Biol 1990, 216: 441\u2013457. 10.1016\/S0022-2836(05)80333-X","journal-title":"J. Mol. Biol"},{"key":"4363_CR12","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1093\/protein\/2.3.185","volume":"2","author":"V Biou","year":"1988","unstructured":"Biou V, Gibrat JF, Levin JM, Robson B, Garnier J: Secondary structure prediction: combination of three different methods. Protein Eng 1988, 2: 185\u2013191. 10.1093\/protein\/2.3.185","journal-title":"Protein Eng"},{"key":"4363_CR13","doi-asserted-by":"publisher","first-page":"371","DOI":"10.1016\/0022-2836(92)90892-N","volume":"227","author":"S Salzberg","year":"1992","unstructured":"Salzberg S, Cost S: Predicting protein secondary structure with a nearest-neighbor algorithm. J. Mol. Biol 1992, 227: 371\u2013374. 10.1016\/0022-2836(92)90892-N","journal-title":"J. Mol. Biol"},{"issue":"12","key":"4363_CR14","doi-asserted-by":"publisher","first-page":"1585","DOI":"10.1093\/bioinformatics\/btg192","volume":"19","author":"KB Li","year":"2003","unstructured":"Li KB: ClustalW-MPI: ClustalW analysis using distributed and parallel computing. Bioinformatics 2003, 19(12):1585\u20131586. 10.1093\/bioinformatics\/btg192","journal-title":"Bioinformatics"},{"key":"4363_CR15","first-page":"1","volume-title":"The technical report from BioTeam Inc","author":"C Dwan","year":"2007","unstructured":"Dwan C: Bioinformatics Benchmarks on the SGI Altix XE Cluster. The technical report from BioTeam Inc 2007, 1\u201313."},{"key":"4363_CR16","first-page":"125","volume":"5","author":"YL Kuo","year":"2003","unstructured":"Kuo YL, Yang CT: Apply Parallel Bioinformatics Applications on Linux PC Clusters. Tunghai Science 2003, 5: 125\u2013141.","journal-title":"Tunghai Science"},{"key":"4363_CR17","first-page":"133","volume":"199","author":"H Rangwala","year":"2005","unstructured":"Rangwala H: Massively Parallel BLAST for the Blue Gene\/L. Proceedings of High Availability and Performance Computing Workshop 2005, 199: 133\u2013154.","journal-title":"Proceedings of High Availability and Performance Computing Workshop"},{"issue":"7","key":"4363_CR18","doi-asserted-by":"publisher","first-page":"1501","DOI":"10.1360\/jos171501","volume":"17","author":"G Tan","year":"2006","unstructured":"Tan G: An optimized and efficiently parallelized dynamic programming for rna secondary structure prediction. Journal of Software 2006, 17(7):1501\u20131509. 10.1360\/jos171501","journal-title":"Journal of Software"},{"key":"4363_CR19","volume-title":"Proceedings of ACM\/IEEE International Conference on SuperComputing (SC\u201906)","author":"G Tan","year":"2006","unstructured":"Tan G: Locality and parallelism optimization for dynamic programming algorithm in bioinformatics. Proceedings of ACM\/IEEE International Conference on SuperComputing (SC\u201906) 2006."},{"key":"4363_CR20","doi-asserted-by":"publisher","first-page":"1669","DOI":"10.1002\/cpe.952","volume":"17","author":"T Liu","year":"2005","unstructured":"Liu T, Schmidt B: Parallel RNA secondary structure prediction using stochastic context-free grammars. Concurrency Computat.: Pract. Exper 2005, 17: 1669\u20131685. 10.1002\/cpe.952","journal-title":"Concurrency Computat.: Pract. Exper"},{"key":"4363_CR21","first-page":"314","volume":"LNCS 4419","author":"B Nilton","year":"2007","unstructured":"Nilton B: Reconfigurable Computing for Accelerating Protein Folding Simulations. Proceedings of IEEE International Workshop on Reconfigurable Computing: Architectures, Tools and Applications (ARC\u201907) 2007, LNCS 4419: 314\u2013325.","journal-title":"Proceedings of IEEE International Workshop on Reconfigurable Computing: Architectures, Tools and Applications (ARC\u201907)"},{"key":"4363_CR22","first-page":"123","volume-title":"Proceedings of IEEE 5th Southern Conference on Programmable Logic (SPL\u201909)","author":"J Advait","year":"2009","unstructured":"Advait J: FPGA Accelerator for Protein Structure Prediction Algorithms. In Proceedings of IEEE 5th Southern Conference on Programmable Logic (SPL\u201909). Edited by: VOR, Stoneham. Butterworth-Heinemann; 2009:123\u2013128."},{"key":"4363_CR23","doi-asserted-by":"publisher","first-page":"6195","DOI":"10.1093\/nar\/gkl789","volume":"34","author":"B Jayaram","year":"2006","unstructured":"Jayaram B: Bhageerath : An energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins. Nucleic Acids Res 2006, 34: 6195\u20136204. 10.1093\/nar\/gkl789","journal-title":"Nucleic Acids Res"},{"key":"4363_CR24","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1016\/S0032-3861(01)00425-6","volume":"43","author":"A Kloczkowski","year":"2002","unstructured":"Kloczkowski A: Protein secondary structure prediction based on the GOR algorithm incorporating multiple sequence alignment information. Polymer 2002, 43: 441\u2013449. 10.1016\/S0032-3861(01)00425-6","journal-title":"Polymer"},{"key":"4363_CR25","unstructured":"The GOR method[\n                    http:\/\/en.wikipedia.org\/wiki\/GORnmethod\n                    \n                  ]"},{"key":"4363_CR26","unstructured":"The GOR-V web Server[\n                    http:\/\/abs.cit.nih.gov\/gor\/\n                    \n                  ]"},{"issue":"17","key":"4363_CR27","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"Altschul","year":"1997","unstructured":"Altschul : Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389\u20133402. 10.1093\/nar\/25.17.3389","journal-title":"Nucleic Acids Res"},{"key":"4363_CR28","unstructured":"General Purpose Microprocessor Power Dissipation Statistic, 2010[\n                    http:\/\/en.wikipedia.org\/wiki\/List_f_CPU_power_dissipation\n                    \n                  ]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-S1-S5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-12-S1-S5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-S1-S5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T05:26:52Z","timestamp":1548221212000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-S1-S5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,2,15]]},"references-count":28,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4363"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-s1-s5","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,2,15]]},"article-number":"S5"}}